International Film Awards2005Daivanamathil - Best Film Award in Spain, Madrid International Film Festival.2000Karunam - Golden Peacock Award, International Film Festival of India- Awards from Federation of International Film Societies, Berlin International Film Fest, Special Mention in Kerala International Film Festival.2000Shantham - Best Cinematography in Festival De 3 Continents, France.1996Desadanam - Special Mention at Karlovy Vary International Film Festival in competition section.[1]

National Film Awards1996Desadanam - Best regional film, Best Audiography, Best Child Artist.1997Kaliyattam - Best Director, Best Actor.2000Karunam - Golden Peacock Award for Best Asian Director, Screenplay.2001Shantham - Best Film, Supporting Actress,2005Daivanamathil - Best Film For National Integration[Nargis dutt],2007 Vellappokkathil - Best Director Short Film.

Notable in his early career were Kudumbasametham (1992), Paithrukam (1993) and Sopanam (1993). Paithrukam was critically acclaimed but was subject to criticism for its conservative, religious philosophy. Desadanam (1997) was a milestone in his career. With the film, he was considered a serious film-maker by the critics. It was followed by another critically acclaimed film, Kaliyattam (1997) which was an adaptation of Shakespere's Othello. It won him the National Film Award for Best Direction.

In 1999 Jayaraj started his nine-film series project Navarasa with Karunam, followed by Shantham(2000). Shantham won the National Film Award for Best Feature Film. The third in the Navarasa series was Bheebhatsa, a Hindi film. A fourth film in the series, Adbutham, is planned and Jayaraj has set his aim to complete the shooting in less than 2 hours 14 minutes with single camera at a time.[4] He reportedly said in an interview to Rediff.com when inquired about the shooting time "In less than ten hours. It may end in five or even two hours. You never know."[5]

Golden Peacock Award, International Film Festival of India- Awards from Federation of International Film Societies, Berlin International Film Fest, Special Mention in Kerala International Film Festival.